The Swiss Football League said in a statement on Wednesday that the decision was taken because the club was suspected of falsifying a bank document produced as a financial guarantee last year.
"The Swiss Football League (SFL) has taken away Neuchatel Xamax's license for participating in championships organised by the SFL," the statement said.
"The disciplinary commission has reached the conclusion that the conditions for the license are no longer met due to the non-presentation of financial guarantees.
"The disciplinary commission is also convinced that the banking guarantee from the Bank of America was not provided by the latter."
Swiss media have reported that the bank letter was littered with basic grammatical and spelling mistakes.
Neuchatel have already had eight points deducted for irregularities in the payment of social security contributions and players' wages.
Chagaev, a businessman who hails from the volatile region of Chechnya, bought the club in May saying he wanted to take Neuchatel into the Champions League.
Since then, he has sacked four coaches, faced a boycott by fans and fired several players.
He also sacked the entire administrative staff, leaving the club unable to print tickets for the opening game of the season, and parted company with all of the club's sponsors.
Chagaev has in turn accused the media of persecuting him because of his nationality.
The club, whose website made no reference to Wednesday's decision but which carries earlier statements saying they feel they are being attacked from many quarters, have five days to appeal.
Neuchatel were formed in 1970 by the merger of two clubs and the team have won the Swiss league twice, in 1987 and 1988.
Their expulsion means the Swiss league, which has reached the halfway mark, will be reduced to nine teams when it resumes in February.
The season has already featured another top flight club, Sion, being deducted 36 points for fielding six players who were signed when the club was subject to a FIFA transfer ban.
FIFA threatened Switzerland with an international suspension after Sion took their case to a civil court.
